Enzyme active-site geometry

SA DePriest, D Mayer, CB Naylor, GR Marshall. 3D-QSAR of angiotensm-convertmg enzyme and thermolysm inhibitors A comparison of CoMEA models based on deduced and experimentally determined active site geometries. I Am Chem Soc 115 5372-5384, 1993. 

The reversibility of halohydrin dehalogenase-catalyzed reactions has been used for the regioselective epoxide-opening with nonnatural nucleophiles (an example is given in Scheme 10.34) [133]. The stereoselectivity of the enzyme results in the resolution of the racemic substrate. At the same time, the regioselectivity imposed by the active site geometry yields the anti-Markovnikov product. [128]... 

One reason for the relatively large RMS deviations, compared to the active sites of MMO and RNR, is that the active-site residues are not coordinated to the selenium (see Figure 2-8). The lack of a structural anchor leads to a relatively unstable active-site geometry. An alternative formulation is that the presence of a metal center with strong ligand interactions is one reason the active-site model works comparatively well for many metal enzymes. 

For the present reaction, the presence of surrounding protein only marginally affects the barrier (it increases by 0.7 kcal/mol). A possible reason for the small protein effects could be that in the present model, the active site is not deeply buried inside the enzyme instead it is located on the interface of two monomers. Still, addition of the protein environment had effects on the active-site geometry. The reason this does not affect the total barrier height is that when comparing transition state and reactant, the protein effect appears to be relatively constant. 

In all the studied systems addition of the surrounding protein in an ONIOM model clearly improves the calculated active-site geometries. This is clearly illustrated in Figure 2-13, which shows the root-mean-square deviation between calculated and experimental structures for four of the studied enzymes. 

The Franck-Condon principle states that there must be no movement of nuclei during an electronic transition therefore, the geometry of the species before and after electron transfer must be unchanged. Consequently, the active site geometry of a redox metalloenzyme must approach that of the appropriate transition state for the electronic transfer. Every known copper enzyme has multiple possible copper oxidation states at its active site, and these are necessary for the enzyme s function. 

DePriest, S.A., Mayer, D., Naylor, C.B., Marshall, G.R. 3D-QSAR of angiotensin-converting enzyme and thermo-lysin inhibitors a comparison of CoMFA models based on deduced and experimentally determned active site geometries./. Am. Chem. Soc. 1993, 3 35, 5372-5384. 

The enzyme can also catalyze the transfer of the terminal phosphoryl of ATP to water i.e., it acts as an ATPase but at a rate 5 x 106 times slower than the above reaction. The basic and nucleophilic properties of water versus the C-6 hydroxyl of glucose are sufficiently similar to suggest no marked differences in rate. Therefore, the explanation of the rate difference is that glucose induces a conformational change that establishes the correct active-site geometry in the enzyme, whereas a water molecule is too small to do so. 

De Priest, S. A., et al. 3D-QSAR of Angiotensin-Converting Enzyme and Thermolysin Inhibitors A Comparison of CoMFA Models Based on Deduced and Experimentally Determined Active-Site Geometries,/. Am. Chem. Soe. 

Fig. 1. The active sites of PT SI and of the A subunits of diphtheria toxin and Escherichia coii heat labile toxin. The thin lines represent the carbon backbones. Only those (3 strands and a helices that are relevant for the active-site geometry are shown. The side chains of residues involved in the enzyme activity, especially those of the catalytic Glu and His residues, are represented by the thick lines. The a2 helix present in PT (top) and coii heat labile toxin (LT, right) is completely missing in diphtheria toxin (DT, left)...

Wang et al. (1994) analyzed by MD the roles of the "double catalytic triad" in papain catalysis, based on the structure of the enzyme, which is not completely known from crystallography (Kamphuis et al., 1984) due to the oxidation state of Cys-25 (present as cysteic acid in the crystal). Stochastic boundary MD (Brooks and Karplus, 1983) was carried out on the whole enzyme + 350 water molecules. Three "layers" were treated according to their distance from the sulfur atom of Cys-25 - atoms within 12A, atoms between 12-16A and the more distant atoms were kept fixed. CHARMM forcefield was employed. The active site geometry was examined as a function of pH, for various mutual states of S-/SH and Im/ImH+. In addition, the mutations of Asp-158 (Menard et al., 1991) were studied. 

Considerable knowledge exists about the nature of the active site of enzymes, their secondary, tertiary, and quaternary structures. In the case of those enzymes that have been obtained in crystalline form and subjected to X-ray analysis, conformational appearance has been deduced. However, the geometry of such an active site, as elucidated on an isolated crystalline enzyme, need not necessarily be complementary to the natural substrate, or drug molecule, to complex and interact with it. Since we visualize such a site as being flexible rather than rigid, the substrate or drug can induce such a complementary fit. 

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